title: Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding.
abstract: BACKGROUND
  Chromatin plays a critical role in regulating transcription factors (TFs) binding to their canonical transcription factor binding sites (TFBS). Recent studies in vertebrates show that many TFs preferentially bind to genomic regions that are well bound by nucleosomes in vitro. Co-occurring secondary motifs sometimes correlated with functional TFBS.
  
  
  RESULTS
  We used a logistic regression to evaluate how well the propensity for nucleosome binding and co-occurrence of a secondary motif identify which canonical motifs are bound in vivo. We used ChIP-seq data for three transcription factors binding to their canonical motifs: c-Jun binding the AP-1 motif (TGA(C)/(G)TCA), GR (glucocorticoid receptor) binding the GR motif (G-ACA---(T)/(C)GT-C), and Hoxa2 (homeobox a2) binding the Pbx (Pre-B-cell leukemia homeobox) motif (TGATTGAT). For all canonical TFBS in the mouse genome, we calculated intrinsic nucleosome occupancy scores (INOS) for its surrounding 150-bps DNA and examined the relationship with in vivo TF binding. In mouse mammary 3134 cells, c-Jun and GR proteins preferentially bound regions calculated to be well-bound by nucleosomes in vitro with the canonical AP-1 and GR motifs themselves contributing to the high INOS. Functional GR motifs are enriched for AP-1 motifs if they are within a nucleosome-sized 150-bps region. GR and Hoxa2 also bind motifs with low INOS, perhaps indicating a different mechanism of action.
  
  
  CONCLUSIONS
  Our analysis quantified the contribution of INOS and co-occurring sequence to the identification of functional canonical motifs in the genome. This analysis revealed an inherent competition between some TFs and nucleosomes for binding canonical TFBS. GR and c-Jun cooperate if they are within 150-bps. Binding of Hoxa2 and a fraction of GR to motifs with low INOS values suggesting they are not in competition with nucleosomes and may function using different mechanisms.
authors.affiliation: Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Ximiao
authors.initials: X
authors.lastname: He
authors.forename: Raghunath
authors.initials: R
authors.lastname: Chatterjee
authors.forename: Sam
authors.initials: S
authors.lastname: John
authors.forename: Hector
authors.initials: H
authors.lastname: Bravo
authors.forename: B K
authors.initials: BK
authors.lastname: Sathyanarayana
authors.forename: Simon C
authors.initials: SC
authors.lastname: Biddie
authors.forename: Peter C
authors.initials: PC
authors.lastname: FitzGerald
authors.forename: John A
authors.initials: JA
authors.lastname: Stamatoyannopoulos
authors.forename: Gordon L
authors.initials: GL
authors.lastname: Hager
authors.forename: Charles
authors.initials: C
authors.lastname: Vinson
mesh_terms: D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly; D004247:DNA / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D016015:Logistic Models; D051379:Mice; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism*; D059372:Nucleotide Motifs; D011485:Protein Binding; D011487:Protein Conformation; D013379:Substrate Specificity; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D002843:Chromatin; D009707:Nucleosomes; D014157:Transcription Factors; D004247:DNA